EBI PDBe MCP Server for WindsurfGive Windsurf instant access to 16 tools to Get Assemblies, Get Binding Sites, Get Cofactors, and more

Name: EBI PDBe
Price: 29 USD
Availability: InStock
Rating: 5.0 (1 reviews)
Author: Vinkius

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Windsurf brings agentic AI coding to a purpose-built IDE. Connect EBI PDBe through Vinkius and Cascade will auto-discover every tool. ask questions, generate code, and act on live data without leaving your editor.

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The EBI PDBe MCP Server for Windsurf is a standout in the The Unthinkable category — giving your AI agent 16 tools to work with, ready to go from day one.

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Classic Setup·json

{
  "mcpServers": {
    "ebi-pdbe": {
      "url": "https://edge.vinkius.com/[YOUR_TOKEN_HERE]/mcp"
    }
  }
}

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About EBI PDBe MCP Server

Connect to the PDBe (Protein Data Bank in Europe) API and access the world's most comprehensive repository of experimentally determined 3D macromolecular structures.

Windsurf's Cascade agent chains multiple EBI PDBe tool calls autonomously. query data, analyze results, and generate code in a single agentic session. Paste Vinkius Edge URL, reload, and all 16 tools are immediately available. Real-time tool feedback appears inline, so you see API responses directly in your editor.

What you can do

Structure Summaries — Get titles, authors, deposition dates, resolution, and experimental methods for any PDB entry
Molecular Entities — Retrieve protein chains, nucleic acids, ligands, their sequences, source organisms, and gene names
Binding Sites & Ligands — Access ligand binding pocket residues, small molecule ligands with formulas and weights
Quality Assessment — Check resolution, R-factors, and overall quality scores for structure reliability
UniProt Mappings — Map between UniProt sequence positions and PDB residue numbers
Biological Assemblies — Understand quaternary structure — monomer, dimer, tetramer, or higher-order complexes
Structure Search — Full-text Solr search across 200+ PDB metadata fields
Publications — Find primary citations, PubMed IDs, and related structural studies

The EBI PDBe MCP Server exposes 16 tools through the Vinkius. Connect it to Windsurf in under two minutes — credentials fully managed, no infrastructure to provision, no vendor lock-in. Your configuration, your data, your control.

All 16 EBI PDBe tools available for Windsurf

When Windsurf connects to EBI PDBe through Vinkius, your AI agent gets direct access to every tool listed below — spanning pdb, protein-structure, 3d-structures, and more. Every call runs in a secure, isolated environment with full audit visibility. Beyond a simple connection, you get real-time monitoring of agent activity, enterprise governance, and optimized token usage.

get

Get assemblies on EBI PDBe

Returns assembly IDs, composition (which entities and how many copies), preferred assembly flag, and form description. Critical for understanding whether a protein functions as a monomer, dimer, tetramer, or higher-order complex. Get biological assembly information (quaternary structure)

get

Get binding sites on EBI PDBe

Critical for drug discovery, molecular docking, and understanding protein-ligand interactions. Get ligand binding site residues and interactions

get

Get cofactors on EBI PDBe

Cofactors like heme, NAD+, FAD, and metal ions are essential for enzyme catalysis and protein function. Get cofactor and prosthetic group annotations

get

Get experiment on EBI PDBe

Get experimental method details for a structure

get

Get ligand monomers on EBI PDBe

Returns chemical component IDs, names, molecular formulas, molecular weights, and their chain/residue positions. Essential for drug discovery and understanding protein-small molecule interactions. Get small molecule ligands bound in the structure

get

Get modified residues on EBI PDBe

Shows the parent compound ID and modification name. Get non-standard amino acids and nucleotides

get

Get molecules on EBI PDBe

Returns entity IDs, molecule types, names, chain assignments, sequence lengths, molecular weights, source organisms, and gene names. Get molecular entities (chains, polymers) in a structure

get

Get mutated residues on EBI PDBe

Shows the original residue, mutated residue, chain, and position. Essential for understanding how the crystallized construct differs from the native protein. Get engineered mutations vs. wild-type sequence

get

Get publications on EBI PDBe

Useful for finding the primary citation and methodology papers for a structure. Get associated journal publications and PubMed IDs

get

Get quality scores on EBI PDBe

The first thing a structural biologist checks when evaluating a structure for reliability. Get global quality metrics for a structure

get

Get related entries on EBI PDBe

Useful for discovering alternative conformations, mutants, or complexes of the same protein that have been structurally characterized. Get related PDB entries citing the same publications

get

Get residue listing on EBI PDBe

Shows residue names, numbers (both PDB and author numbering), organized by entity and chain. Returns a sample of the first 20 residues per chain for efficiency. Get full residue-level inventory per chain

get

Get secondary structure on EBI PDBe

Shows the count of helices and strands per chain, organized by molecular entity. Essential for understanding protein fold topology. Get helix, sheet, and coil assignments per residue

get

Get summary on EBI PDBe

Use a 4-character PDB ID such as 1cbs, 4hhb, 6lu7. Get PDB entry summary with title, authors, and resolution

get

Get uniprot mapping on EBI PDBe

Returns UniProt accessions, chain assignments, and start/end position mappings. Essential for cross-referencing between protein sequence databases and 3D structural data. Get UniProt to PDB residue mappings

Search structures on EBI PDBe

Use natural language queries like "insulin receptor kinase", "SARS-CoV-2 spike protein", "cryo-EM resolution<3", or specific organism names. Returns PDB IDs, titles, methods, resolutions, and organisms. Search PDB structures with full-text queries

Connect EBI PDBe to Windsurf via MCP

Follow these steps to wire EBI PDBe into Windsurf. The entire setup takes under two minutes — your credentials stay safe behind Vinkius.

Open MCP Settings

Go to Settings → MCP Configuration or press Cmd+Shift+P and search "MCP"

Add the server

Paste the JSON configuration above into mcp_config.json

Save and reload

Windsurf will detect the new server automatically

Start using EBI PDBe

Open Cascade and ask: "Using EBI PDBe, help me...". 16 tools available

Why Use Windsurf with the EBI PDBe MCP Server

Windsurf provides unique advantages when paired with EBI PDBe through the Model Context Protocol.

Windsurf's Cascade agent autonomously chains multiple tool calls in sequence, solving complex multi-step tasks without manual intervention

Purpose-built for agentic workflows. Cascade understands context across your entire codebase and integrates MCP tools natively

JSON-based configuration means zero code changes: paste a URL, reload, and all 16 tools are immediately available

Real-time tool feedback is displayed inline, so you see API responses directly in your editor without switching contexts

EBI PDBe + Windsurf Use Cases

Practical scenarios where Windsurf combined with the EBI PDBe MCP Server delivers measurable value.

Automated code generation: ask Cascade to fetch data from EBI PDBe and generate models, types, or handlers based on real API responses

Live debugging: query EBI PDBe tools mid-session to inspect production data while debugging without leaving the editor

Documentation generation: pull schema information from EBI PDBe and have Cascade generate comprehensive API docs automatically

Rapid prototyping: combine EBI PDBe data with Cascade's code generation to scaffold entire features in minutes

Example Prompts for EBI PDBe in Windsurf

Ready-to-use prompts you can give your Windsurf agent to start working with EBI PDBe immediately.

"Show me the structure summary and quality of the SARS-CoV-2 main protease (6lu7)."

"What ligands are bound in the hemoglobin structure 4hhb?"

"Search for cryo-EM structures of ribosome complexes."

Troubleshooting EBI PDBe MCP Server with Windsurf

Common issues when connecting EBI PDBe to Windsurf through Vinkius, and how to resolve them.

Server not connecting

Check Settings → MCP for the server status. Try toggling it off and on.

EBI PDBe + Windsurf FAQ

Common questions about integrating EBI PDBe MCP Server with Windsurf.

How does Windsurf discover MCP tools?

Windsurf reads the mcp_config.json file on startup and connects to each configured server via Streamable HTTP. Tools are listed in the MCP panel and available to Cascade automatically.

Can Cascade chain multiple MCP tool calls?

Yes. Cascade is an agentic system. it can plan and execute multi-step workflows, calling several tools in sequence to accomplish complex tasks without manual prompting between steps.

Does Windsurf support multiple MCP servers?

Yes. Add as many servers as needed in mcp_config.json. Each server's tools appear in the MCP panel and Cascade can use tools from different servers in a single flow.